PDB Short entry for 107D HEADER DNA 17-JAN-95 107D TITLE SOLUTION STRUCTURE OF THE COVALENT DUOCARMYCIN A-DNA DUPLEX COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*CP*TP*TP*TP*TP*C)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*GP*AP*AP*AP*AP*GP*G)-3'); COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: CHEMICALLY SYNTHESIZED; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 OTHER_DETAILS: CHEMICALLY SYNTHESIZED KEYWDS DNA, DOUBLE HELIX EXPDTA SOLUTION NMR NUMMDL 4 AUTHOR C.H.LIN,D.J.PATEL REVDAT 5 13-MAR-24 107D 1 COMPND SOURCE REVDAT 4 16-FEB-22 107D 1 REMARK REVDAT 3 07-APR-09 107D 1 REMARK REVDAT 2 24-FEB-09 107D 1 VERSN REVDAT 1 08-MAY-95 107D 0 JRNL AUTH C.H.LIN,D.J.PATEL JRNL TITL SOLUTION STRUCTURE OF THE COVALENT DUOCARMYCIN A-DNA DUPLEX JRNL TITL 2 COMPLEX. JRNL REF J.MOL.BIOL. V. 248 162 1995 JRNL REFN ISSN 0022-2836 JRNL PMID 7731041 JRNL DOI 10.1006/JMBI.1995.0209 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: TWO STARTING STRUCTURES WERE GENERATED REMARK 3 BY MANUALLY DOCKING THE DRUG ONTO A- AND B-FORM DNA USING REMARK 3 INSIGHT II AND WERE SUBSEQUENTLY REFINED BY DISTANCE-RESTRAINED REMARK 3 MOLECULAR DYNAMICS USING A SET OF INTER-PROTON DISTANCE REMARK 3 RESTRAINTS DERIVED FROM THE 2-D NMR DATA. ONE INITIAL VELOCITY REMARK 3 SEED WAS USED FOR EACH STARTING STRUCTURE WHICH YIELDS TWO REMARK 3 DISTANCE-REFINED STRUCTURES. THEY WERE REFINED FURTHER WITH TWO REMARK 3 INITIAL VELOCITIES USING RELAXATION-MATRIX BASED NOE INTENSITY- REMARK 3 RESTRAINED MOLECULAR DYNAMICS TO GENERATE THE FINAL FOUR REMARK 3 STRUCTURES. THE FINAL FOUR STRUCTURES WERE OBTAINED BY TAKING REMARK 3 THE AVERAGE COORDINATES OF THE LAST 1.0 PS OF THE DYNAMICS REMARK 3 DURING RELAXATION MATRIX REFINEMENT AND ENERGY MINIMIZED. THE REMARK 3 R(1/6) VALUE WAS USED TO REFINE THE STRUCTURE DURING RELAXATION REMARK 3 MATRIX REFINEMENT. THE SUMMATIONS RUN THROUGH ALL OBSERVED, REMARK 3 QUANTIFIABLE NOE CROSSPEAKS IN NOESY SPECTRA RECORDED IN D2O AND REMARK 3 MIXING TIMES OF 40, 80, 120 AND 160 MS. THE R(1/6) FACTOR AND REMARK 3 THE RMS DEVIATIONS FROM IDEAL GEOMETRY FOR THE FOUR FINAL REMARK 3 STRUCTURES ARE: MODEL1-MODEL4 R(1/6) FACTOR 0.042-0.045 BOND REMARK 3 (ANG) 0.009-0.010 ANGLES (DEG) 3.078-3.780 IMPROPERS (DEG) 0.310- REMARK 3 0.321. THE STRUCTURE HAS APPROXIMATE TWO-FOLD SYMMETRY RELATING REMARK 3 THE TWO STRANDS OF THE DNA WITH THE SYMMETRY AXIS PERPENDICULAR REMARK 3 TO THE HELICAL AXIS. THE TRANSFORMATION MATRIX WAS CALCULATED REMARK 3 FOR THE AVERAGED STRUCTURE OF THE FOUR MODELS. REMARK 4 REMARK 4 107D COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000170017. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : NULL REMARK 210 PH : NULL REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : NULL REMARK 210 SPECTROMETER MODEL : NULL REMARK 210 SPECTROMETER MANUFACTURER : NULL REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : MOLECULAR DYNAMICS, MATRIX REMARK 210 RELAXATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 4 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: DUOCARMYCIN A WAS PROVIDED BY KYOWA HAKKO KOGYO CO., REMARK 210 JAPAN. REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 N3 DA B 12 C10 DUO B 15 1.41 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 1 DT A 5 C5 DT A 5 C7 0.041 REMARK 500 2 DT A 3 C5 DT A 3 C7 0.038 REMARK 500 2 DT A 4 C5 DT A 4 C7 0.037 REMARK 500 2 DT A 5 C5 DT A 5 C7 0.048 REMARK 500 2 DT A 6 C5 DT A 6 C7 0.036 REMARK 500 4 DT A 3 C5 DT A 3 C7 0.040 REMARK 500 4 DT A 5 C5 DT A 5 C7 0.039 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 1 DC A 1 O4' - C1' - C2' ANGL. DEV. = -5.5 DEGREES REMARK 500 1 DC A 1 O4' - C1' - N1 ANGL. DEV. = 9.3 DEGREES REMARK 500 1 DC A 2 N1 - C2 - O2 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DT A 3 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 1 DT A 3 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DT A 4 C5' - C4' - O4' ANGL. DEV. = 8.5 DEGREES REMARK 500 1 DT A 4 N3 - C2 - O2 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DT A 4 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DT A 5 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DT A 6 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DT A 6 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DG B 8 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DA B 10 O4' - C1' - N9 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 DA B 12 O4' - C1' - C2' ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DA B 12 O4' - C1' - N9 ANGL. DEV. = 5.9 DEGREES REMARK 500 1 DG B 13 C3' - O3' - P ANGL. DEV. = 8.5 DEGREES REMARK 500 1 DG B 14 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES REMARK 500 2 DC A 1 O4' - C1' - C2' ANGL. DEV. = -5.2 DEGREES REMARK 500 2 DC A 1 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 2 DC A 2 O4' - C4' - C3' ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DC A 2 N1 - C2 - O2 ANGL. DEV. = 4.2 DEGREES REMARK 500 2 DT A 3 C3' - O3' - P ANGL. DEV. = 7.5 DEGREES REMARK 500 2 DT A 4 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DA B 10 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DA B 12 O4' - C1' - N9 ANGL. DEV. = 5.8 DEGREES REMARK 500 2 DG B 13 C3' - O3' - P ANGL. DEV. = 8.1 DEGREES REMARK 500 2 DG B 14 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 3 DC A 1 O4' - C1' - C2' ANGL. DEV. = -5.3 DEGREES REMARK 500 3 DC A 1 O4' - C1' - N1 ANGL. DEV. = 9.9 DEGREES REMARK 500 3 DC A 2 N1 - C2 - O2 ANGL. DEV. = 3.6 DEGREES REMARK 500 3 DT A 3 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 3 DT A 4 C5' - C4' - O4' ANGL. DEV. = 7.4 DEGREES REMARK 500 3 DT A 4 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 3 DG B 8 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 3 DA B 10 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 3 DA B 12 O4' - C1' - C2' ANGL. DEV. = -6.4 DEGREES REMARK 500 3 DA B 12 O4' - C1' - N9 ANGL. DEV. = 6.1 DEGREES REMARK 500 3 DG B 13 C3' - O3' - P ANGL. DEV. = 9.0 DEGREES REMARK 500 3 DG B 14 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 4 DC A 1 O4' - C1' - C2' ANGL. DEV. = -4.9 DEGREES REMARK 500 4 DC A 1 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 4 DC A 2 O4' - C4' - C3' ANGL. DEV. = 3.7 DEGREES REMARK 500 4 DC A 2 N1 - C2 - O2 ANGL. DEV. = 4.2 DEGREES REMARK 500 4 DT A 3 C3' - O3' - P ANGL. DEV. = 7.9 DEGREES REMARK 500 4 DT A 6 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 4 DC A 7 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES REMARK 500 4 DG B 8 C3' - O3' - P ANGL. DEV. = 8.2 DEGREES REMARK 500 4 DA B 9 O4' - C1' - N9 ANGL. DEV. = 6.2 DEGREES REMARK 500 4 DA B 9 C3' - O3' - P ANGL. DEV. = 7.8 DEGREES REMARK 500 4 DA B 10 O4' - C1' - N9 ANGL. DEV. = 6.2 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 55 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DUO B 15 DBREF 107D A 1 7 PDB 107D 107D 1 7 DBREF 107D B 8 14 PDB 107D 107D 8 14 SEQRES 1 A 7 DC DC DT DT DT DT DC SEQRES 1 B 7 DG DA DA DA DA DG DG HET DUO B 15 63 HETNAM DUO 4-HYDROXY-2,8-DIMETHYL-1-OXO-6-(4,5,6-TRIMETHOXY-1H- HETNAM 2 DUO INDOLE-2-CARBONYL)-1,2,3,6,7,8-HEXAHYDRO-3,6-DIAZA-AS- HETNAM 3 DUO INDACENE-2-CARBOXYLIC ACID METHYL ESTER HETSYN DUO DUOCARMYCIN A FORMUL 3 DUO C26 H27 N3 O8 SITE 1 AC1 9 DT A 4 DT A 5 DT A 6 DC A 7 SITE 2 AC1 9 DA B 10 DA B 11 DA B 12 DG B 13 SITE 3 AC1 9 DG B 14 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000